Mandy LiuDepartment of Pharmaceutical Sciences and Center for Advancement of Drug Research, College of Pharmacy, Western University of Health Sciences, Pomona, CA, USABMC Complement Altern Med 13:11. 2013

Maximum predictive power of the microarray-based models for clinical outcomes is limited by correlation between endpoint and gene expression profile

Chen ZhaoThe Center for Bioinformatics and The institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, ChinaBMC Genomics 12:S3. 2011

Effect of training-sample size and classification difficulty on the accuracy of genomic predictors

Mandy LiuDepartment of Pharmaceutical Sciences and Center for Advancement of Drug Research, College of Pharmacy, Western University of Health Sciences, Pomona, CA, USABMC Complement Altern Med 13:11. 2013

..In our previous study, the microarray gene expression profiles of SWT on breast cancer cell line MCF-7 were found similar to the effect of β-estradiol (E2) on MCF-7 cells in the Connectivity Map database...

Maximum predictive power of the microarray-based models for clinical outcomes is limited by correlation between endpoint and gene expression profile

Chen ZhaoThe Center for Bioinformatics and The institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, ChinaBMC Genomics 12:S3. 2011

..Fine-tuning of model parameters and optimizing each step of the modeling process often results in over-fitting problems without improving performance...

Effect of training-sample size and classification difficulty on the accuracy of genomic predictors

..The resultant variety of existing and emerging methods exacerbates confusion and continuing debate in the microarray community on the appropriate choice of methods for identifying reliable DEG lists...

..Microarray-based measurement of mRNA abundance assumes a linear relationship between the fluorescence intensity and the dye concentration. In reality, however, the calibration curve can be nonlinear...

QA/QC: challenges and pitfalls facing the microarray community and regulatory agencies

..To evaluate whether microarray analysis can be used for distinguishing the tissue-specific carcinogenicity of AA, we examined gene expression profiles in kidney and liver of rats treated with carcinogenic doses of AA...

Development of public toxicogenomics software for microarray data management and analysis

..ArrayTrack is publicly available online ( http://www.fda.gov/nctr/science/centers/toxicoinformatics/ArrayTrack/index.htm ) and the prospective user can also request a local installation version by contacting the authors...

Self-self hybridization as an alternative experiment design to dye swap for two-color microarrays

..In this paper, we analyzed both the batch size and batch composition for effects on the genotype calling algorithm BRLMM using raw data of 270 HapMap samples analyzed with the Affymetrix Human Mapping 500 K array set...

Analysis of gene expression changes in relation to toxicity and tumorigenesis in the livers of Big Blue transgenic rats fed comfrey (Symphytum officinale)

..Our previous study suggested that comfrey induces liver tumors by a genotoxic mechanism and that the pyrrolizidine alkaloids in the plant are responsible for mutation induction and tumor initiation in rat liver...

Mold(2), molecular descriptors from 2D structures for chemoinformatics and toxicoinformatics

..High reproducibility and reliability are expected because Mold (2) does not require 3D structures. Mold (2) is freely available to the public ( http://www.fda.gov/nctr/science/centers/toxicoinformatics/index.htm)...

..9941 was achieved. This study demonstrates that SVM based methods can accurately recognize and predict the protein family to which a sequence belongs based solely on its primary amino acid sequence...

Huixiao HongCenter of Excellence for Bioinformatics, Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arizona, United States of AmericaPLoS ONE 7:e44483. 2012

..Using ArrayTrack, we can select an analysis method from the TOOL and apply the method to selected microarray data stored in the MicroarrayDB; the analysis results can be linked directly to gene information in the LIB...

..Relative noise was estimated for both data sets, and the results were consistent with the observations in the original papers, demonstrating the proposed method is reliable for estimating relative noise in microarray data. ..

..This multiplatform investigation of the behavior and utility of ERCs provides a basis for articulating specific recommendations for their future use in evaluating assay performance across multiple platforms...

..ArrayTrack is used in the routine review of genomic data submitted to the FDA; here, three hypothetical examples of its use in the Voluntary eXploratory Data Submission (VXDS) program are illustrated.: ..

..All data are available free of cost and the reference RNA samples are available for proficiency testing. Thus, current microarray technology appears to provide both reliability and consistency for regulatory submissions...

Phytoestrogens and mycoestrogens bind to the rat uterine estrogen receptor

..00008; E(2) = 100). These data can be utilized before animal testing to rank order estimates of the potential for in vivo estrogenic activity of a wide range of untested plant chemicals (as well as other chemicals) based on ER binding...

..The studies of abacavir-induced HSR and the implementation of the HLA-B*57:01 screening in the clinic represent a successful example of the use of pharmacogenetics for personalized diagnosis and therapy...

Investigation of reproducibility of differentially expressed genes in DNA microarrays through statistical simulation

..g., median lethal dose [LD50] dose). The reader is also referred to a companion paper in this issue that discusses quantitative structure-activity relationship (QSAR) methods that have advanced markedly over the past decade...

A testing strategy to predict risk for drug-induced liver injury in humans using high-content screen assays and the 'rule-of-two' model

..In summary, titration samples may be regarded as a valuable tool, not only for assessing microarray platform performance and different analysis methods, but also for determining some underlying biological features of the samples...

..It is important to investigate the multi-scale biological system in a systematic way to better understand the gene regulation networks and signal transduction pathways involved in the cellular responses to environmental factors...

..The method to construct virtual combinatorial library using SMILES strings was further visualized by Visual Basic.net that can facilitate the needs of generating other type virtual combinatorial libraries...

Design, synthesis, and evaluation of a new class of noncyclic 1,3-dicarbonyl compounds as PPARalpha selective activators

..614 for AM1 and 0.822 for PM3 methods, set a successful example for applying a similar approach in building QSAR models for PPARalpha and -delta that could potentially offer a new opportunity in the design of novel PPAR modulators...